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Bioinformatics Advance Access published online on September 10, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn480
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

Alan P. Boyle 1, Justin Guinney 1, Gregory E. Crawford 1 and Terrence S. Furey 1,*

1Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708

*To whom correspondence should be addressed. Dr. Terrence S. Furey, E-mail: terry.furey{at}duke.edu


  Abstract

Summary: Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Availability: The software is written in the Java language and is available on all major computing platforms for download at http://www.genome.duke.edu/labs/furey/software/fseq.

Contact: terry.furey{at}duke.edu

Associate Editor: Prof. Alfonso Valencia

Received on June 30, 2008; revised on August 18, 2008; accepted on September 7, 2008

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